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US7371758B2 - Antimalarial pyrimidine derivatives and methods of making and using them - Google Patents

Antimalarial pyrimidine derivatives and methods of making and using them Download PDF

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US7371758B2
US7371758B2 US10/386,613 US38661303A US7371758B2 US 7371758 B2 US7371758 B2 US 7371758B2 US 38661303 A US38661303 A US 38661303A US 7371758 B2 US7371758 B2 US 7371758B2
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diamino
pyrimidine
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Yongyuth Yuthavong
Bongkoch Tarnchompoo
Sumalee Kamchonwongpaisan
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D239/00—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings
    • C07D239/02—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings
    • C07D239/24—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members
    • C07D239/28—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, directly attached to ring carbon atoms
    • C07D239/46—Two or more oxygen, sulphur or nitrogen atoms
    • C07D239/48—Two nitrogen atoms
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D239/00—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings
    • C07D239/02—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings
    • C07D239/24—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members
    • C07D239/28—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, directly attached to ring carbon atoms
    • C07D239/46—Two or more oxygen, sulphur or nitrogen atoms
    • C07D239/48—Two nitrogen atoms
    • C07D239/49—Two nitrogen atoms with an aralkyl radical, or substituted aralkyl radical, attached in position 5, e.g. trimethoprim
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • DHFR dihydrofolate reductase
  • 2,4-diaminopyrimidine derivative compounds have been synthesized and shown to have antimalarial activities. These compounds include pyrimethamine (Pyr) and derivatives thereof, with substituents on the 5-phenyl group, and substituents on position 6.
  • the synthetic processes generally involve three steps: a) preparation of keto nitrile via an acylation of the arylacetonitrile with ester as catalyzed by an alkali alkoxide, b) preparation of the corresponding ⁇ -alkoxyacrylonitrile or the corresponding ketal of the keto nitrile, c) preparation of 2,4-diaminopyrimidine by treatment of the above intermediate with guanidine in alcoholic solution.
  • the present invention provides a modified method, employing effective acylating reagents, base, reaction conditions and solvents in three steps, for the preparation of pyrimethamine derivative compounds in better overall yields.
  • pyrimethamine and other described 2,4-diaminopyrimidine derivative compounds are effective against wild type malaria parasites, they are not effective against resistant parasites, which have been shown to bear mutations in the dihydrofolate reductase, for examples, mutations of Plasmodium falciparum dihydrofolate reductase at positions 108 (serine to asparagine), 51 (asparagine to isoleucine), 59 (cysteine to arginine) and 164 (isoleucine to leucine).
  • the degree of resistance generally increases with the number of mutations the parasite accumulates, prompting the need for novel drugs which are effective both against sensitive and resistant strains of malaria parasites.
  • These drugs must, moreover, be of low toxicity to the human host. It is also preferable that these drugs do not have significant antibacterial activity, since they often have to be administered over extended periods. Under such circumstances, there would be a danger of development of resistant strains of bacteria if the drugs also have significant antibacterial activity.
  • the present invention describes compounds which are effective against malaria, in particular drug-resistant malaria arising from mutations as described.
  • a number of these compounds have low toxicity to the human host and are therefore useful in suitable pharmaceutical compositions. They have little antibacterial activities and are unlikely to lead to development of resistant strains of bacteria on deployment. The procedure for their synthesis is also described.
  • This invention meets the need for more effective compounds against malaria, in particular drug-resistant malaria specifically arising from resistance to inhibition of the parasite dihydrofolate reductase by antifolate drugs.
  • This invention provides compounds of formula (I) wherein R 1 represents a hydrogen atom or a 3-halogen atom, and R 2 represents a straight-chain alkyl group containing up to 6 carbon atoms, a straight-chain alkyl group containing up to 3 carbon atoms with unsubstituted or substituted aromatic ring, or alkoxycarbonyl substituent at the end position, or aryloxyalkoxyalkyl group.
  • Methods for synthesis of the above compounds comprise three steps: a) acylation of arylacetonitrile (II) with acid chloride (III) employing lithium diisopropylamide in tetrahydrofuran at ⁇ 78° C. affords the desired keto nitrile (IV); b) reaction of keto nitrile (IV) with diazomethane in dioxane at room temperature affords the corresponding ⁇ -methoxyacrylonitrile (V); c) condensation reaction of the ⁇ -methoxyacrylonitrile (V) with guanidine in dimethyl sulfoxide at 80° C. provides the desired pyrimethamine derivative compound (I).
  • This invention provides methods for therapeutically and/or prophylactically using the compounds described, and pharmaceutically acceptable salts and products thereof.
  • FIG. 1 shows a schematic diagram of preparation method of 2,4-diaminopyrimidine derivative compounds of formula I.
  • a modified method shown in FIG. 1 has been employed for the preparation of 2,4-diaminopyrimidine derivative compounds of the general formula (I), wherein R 1 represents a hydrogen atom or a 3-halogen atom, and R 2 represents a straight-chain alkyl group containing up to 6 carbon atoms, a straight-chain alkyl group containing up to 3 carbon atoms with unsubstituted or substituted aromatic ring, or alkoxycarbonyl substituent at the end position, or aryloxyalkoxyalkyl group.
  • R 1 represents a hydrogen atom or a 3-halogen atom
  • R 2 represents a straight-chain alkyl group containing up to 6 carbon atoms, a straight-chain alkyl group containing up to 3 carbon atoms with unsubstituted or substituted aromatic ring, or alkoxycarbonyl substituent at the end position, or aryloxyalkoxyalkyl group.
  • Diazomethane gas generated from a reaction of diazald and sodium hydroxide solution, was passed into a solution of keto nitrile (IV) (5 mmol) in cold dioxane (10 mL). The reaction mixture was left at room temperature overnight and evaporated to dryness under reduced pressure to give the corresponding ⁇ -methoxyacrylonitrile (V) in quantitative yield. The crude product was further used in the next step without purification.
  • Enzymes comprising dihydrofolate reductase of Plasmodium falciparum , wild type, single (S108N), double (C59R+S108N), triple (N51+C59R+S108N, C59R+S108N+1164L), and quadruple (N51+C59R+S108N+I164L) mutants, were prepared from E. coli expression system ( E. coli BL21 (DE3)pLysS) containing the corresponding genes.
  • the activity of the enzymes was determined spectrophotometrically at 25° C.
  • the reaction (1 mL) contained 1 ⁇ DHFR buffer (50 mM TES, pH 7.0, 75 mM ⁇ -mercaptoethanol, 1 mg/mL Bovine Serum Albumin), 100 ⁇ M each of the substrate dihydrofolate and cofactor NADPH, and appropriate amount of affinity-purified enzyme to initiate the reaction (0.001-0.005 units in phosphate buffer containing 50 mM KCl).
  • the inhibition of the enzymes with the invented compounds was investigated in a 96 well plate with 200 ⁇ L of the above mixture in the presence of antifolate. The kinetics was followed at 340 nm.
  • P. falciparum strains were used in this study. P. falciparum strains were maintained continuously in human erythrocytes at 37° C. under 3% CO 2 in RPMI 1640 culture media supplemented with 25 mM HEPES, pH 7.4, 0.2% NaHCO 3 , 40 ⁇ g/mL gentamicin and 10% human serum.
  • In vitro antimalarial activity was determined by using [ 3 H]-hypoxanthine incorporation method.
  • the drugs were initially dissolved in DMSO and diluted with the culture media. Aliquots (25 ⁇ L) of the drug of different concentrations were dispensed in 96-well plates and 200 ⁇ L of 1.5% cell suspension of parasitized erythrocytes containing 1-2% parasitemia were added. The final concentration of DMSO (0.1%) did not affect the parasite growth. The mixtures were incubated in a 3% CO 2 incubator at 37° C. After 24 h of incubation, 25 ⁇ L (0.25 ⁇ Ci) of [ 3 H]-hypoxanthine were added to each well.
  • the parasite cultures were further incubated under the same condition for 18-24 h.
  • DNA of parasites was harvested onto glass filter paper.
  • the filters were air-dried and 20 ⁇ L liquid scintillation fluid was added. The radioactivity on the filters was then measured using a microplate scintillation counter.
  • the concentration of inhibitor which inhibited 50% of the parasite growth was determined from the sigmoidal curve obtained by plotting the percentages of [ 3 H]-hypoxanthine incorporation against drug concentrations. Examples of the invented compounds in this series with active antimalarial activity against wild type and in particular against parasites carrying single, double, triple, and quadruple mutant enzymes are as summarized in Table 2.
  • Antibacterial activity of the invented compounds was determined by incubation of suspension of bacteria, Staphylococcus aureus and E. coli with a serial dilution of the drugs for 20 hours in a 96-well plate. Bacterial growth inhibition was determined by spectrophotometer at 600 nm. The IC 50 -values was determined from the sigmoidal curve obtained by plotting the percentages of bacterial growth against drug concentrations.

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Abstract

Compounds of the formula (I) wherein R1 represents a hydrogen atom or a 3-halogen atom, and R2 represents a straight-chain alkyl group containing up to 6 carbon atoms, a straight-chain alkyl group containing up to 3 carbon atoms with unsubstituted or substituted aromatic ring, or alkoxycarbonyl substituent at the end position, or aryloxyalkoxyalkyl group have been found to possess antimalarial activity against Plasmodium falciparum lines, including those resistant against pyrimethamine and other antifolates. The compounds themselves, methods of making these compounds, and methods of using these compounds are all disclosed.

Description

CROSS-REFERENCE TO RELATED APPLICATION
Not Applicable
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
Not Applicable
REFERENCE TO SEQUENCE LISTING
Not Applicable
BACKGROUND OF THE INVENTION
The 2,4-diaminopyrimidine derivative compounds have been extensively studied as inhibitors of dihydrofolate reductase (DHFR). In the living cell, DHFR reduces dihydrofolate to tetrahydrofolate, which is further used to produce 5,10-methylenetetrahydrofolate, a substance essential for DNA synthesis and cell growth. Inhibition of DHFR results in inhibition of DNA synthesis, and in cell death. Many DHFR inhibitors, also known as antifolates, are therefore potentially useful drugs against infectious agents, provided that they can specifically inhibit DHFR of the target cells without substantially affecting the cells of the host.
Many 2,4-diaminopyrimidine derivative compounds have been synthesized and shown to have antimalarial activities. These compounds include pyrimethamine (Pyr) and derivatives thereof, with substituents on the 5-phenyl group, and substituents on position 6. The synthetic processes generally involve three steps: a) preparation of keto nitrile via an acylation of the arylacetonitrile with ester as catalyzed by an alkali alkoxide, b) preparation of the corresponding β-alkoxyacrylonitrile or the corresponding ketal of the keto nitrile, c) preparation of 2,4-diaminopyrimidine by treatment of the above intermediate with guanidine in alcoholic solution. Due to low yield of keto nitrile together with decomposed/polymerized compounds of the previous methods, the present invention provides a modified method, employing effective acylating reagents, base, reaction conditions and solvents in three steps, for the preparation of pyrimethamine derivative compounds in better overall yields.
Although pyrimethamine and other described 2,4-diaminopyrimidine derivative compounds are effective against wild type malaria parasites, they are not effective against resistant parasites, which have been shown to bear mutations in the dihydrofolate reductase, for examples, mutations of Plasmodium falciparum dihydrofolate reductase at positions 108 (serine to asparagine), 51 (asparagine to isoleucine), 59 (cysteine to arginine) and 164 (isoleucine to leucine). The degree of resistance generally increases with the number of mutations the parasite accumulates, prompting the need for novel drugs which are effective both against sensitive and resistant strains of malaria parasites. These drugs must, moreover, be of low toxicity to the human host. It is also preferable that these drugs do not have significant antibacterial activity, since they often have to be administered over extended periods. Under such circumstances, there would be a danger of development of resistant strains of bacteria if the drugs also have significant antibacterial activity.
The present invention describes compounds which are effective against malaria, in particular drug-resistant malaria arising from mutations as described. A number of these compounds have low toxicity to the human host and are therefore useful in suitable pharmaceutical compositions. They have little antibacterial activities and are unlikely to lead to development of resistant strains of bacteria on deployment. The procedure for their synthesis is also described.
BRIEF SUMMARY OF THE INVENTION
This invention meets the need for more effective compounds against malaria, in particular drug-resistant malaria specifically arising from resistance to inhibition of the parasite dihydrofolate reductase by antifolate drugs. This invention provides compounds of formula (I) wherein R1 represents a hydrogen atom or a 3-halogen atom, and R2 represents a straight-chain alkyl group containing up to 6 carbon atoms, a straight-chain alkyl group containing up to 3 carbon atoms with unsubstituted or substituted aromatic ring, or alkoxycarbonyl substituent at the end position, or aryloxyalkoxyalkyl group.
Methods for synthesis of the above compounds are also disclosed which comprise three steps: a) acylation of arylacetonitrile (II) with acid chloride (III) employing lithium diisopropylamide in tetrahydrofuran at −78° C. affords the desired keto nitrile (IV); b) reaction of keto nitrile (IV) with diazomethane in dioxane at room temperature affords the corresponding β-methoxyacrylonitrile (V); c) condensation reaction of the β-methoxyacrylonitrile (V) with guanidine in dimethyl sulfoxide at 80° C. provides the desired pyrimethamine derivative compound (I).
This invention provides methods for therapeutically and/or prophylactically using the compounds described, and pharmaceutically acceptable salts and products thereof.
It is an object of this invention to provide 2,4-diaminopyrimidine derivative compounds, and pharmaceutically acceptable salts thereof, for substantially inhibiting dihydrofolate reductase enzymes.
It is an object of this invention to provide 2,4-diaminopyrimidine derivative compounds, and pharmaceutically acceptable salts thereof, having antimalarial activity, including activity against drug-resistant malaria both by themselves and in synergistic combinations with sulfonamides and/or other agents.
It is an object of this invention to provide methods for synthesizing 2,4-diaminopyrimidine derivative compounds, and pharmaceutically acceptable salts thereof.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING
FIG. 1 shows a schematic diagram of preparation method of 2,4-diaminopyrimidine derivative compounds of formula I.
 DETAILED DESCRIPTION OF THE INVENTION 1. Preparation of 2,4-Diaminopyrimidine Derivative Compounds
In the present invention, a modified method shown in FIG. 1 has been employed for the preparation of 2,4-diaminopyrimidine derivative compounds of the general formula (I), wherein R1 represents a hydrogen atom or a 3-halogen atom, and R2 represents a straight-chain alkyl group containing up to 6 carbon atoms, a straight-chain alkyl group containing up to 3 carbon atoms with unsubstituted or substituted aromatic ring, or alkoxycarbonyl substituent at the end position, or aryloxyalkoxyalkyl group.
Figure US07371758-20080513-C00001
The modified method said above is described in detail below.
1.1 Preparation of Keto Nitrile (III)
To a solution of lithium diisopropylamide (20 mmol, 1 equivalent) in tetrahydrofuran (30 mL) at −78° C. was added slowly a solution of arylacetonitrile (II) (20 mmol, 1 equivalent) in tetrahydrofuran (30 mL) and the reaction mixture was left stirring at −78° C. for 1 hour. A solution of acid chloride (III) (20 mmol, 1 equivalent) in tetrahydrofuran (5 mL) was added into the reaction at −78° C. After quenching with saturated aqueous ammonium chloride solution, the crude mixture was extracted three times with dichloromethane. The combined dichloromethane extracts were successively washed with water, saturated aqueous sodium chloride solution, dried over magnesium sulfate, filtered, and evaporated to dryness under reduced pressure. Purification of the crude product by column chromatography gave the desired keto nitrile (IV).
1.2 Preparation of β-Methoxyacrylonitrile (V)
Diazomethane gas, generated from a reaction of diazald and sodium hydroxide solution, was passed into a solution of keto nitrile (IV) (5 mmol) in cold dioxane (10 mL). The reaction mixture was left at room temperature overnight and evaporated to dryness under reduced pressure to give the corresponding β-methoxyacrylonitrile (V) in quantitative yield. The crude product was further used in the next step without purification.
1.3 Condensation Reaction of the β-Methoxyacrylonitrile (V) with Guanidine
A mixture of β-methoxyacrylonitrile (IV) (3 mmol) and guanidine (5 mmol) in dimethyl sulfoxide (5 mL) was heated at 80° C. for 5 min under N2. The reaction mixture was poured into cold water. The precipitate obtained was collected by filtration and washed successively with water. Recrystallization from ethanol gave white crystals of 2,4-diaminopyrimidine derivative compounds (I).
As the result of the said procedure above, the invented compounds have been generated and some are listed below.
EXAMPLE 1
2,4-diamino-6-(n-hexyl)-5-phenylpyrimidine white crystals, mp 155-156° C., 1H (400 MHz, DMSO-d6) 6 0.77 (t, J=7.5Hz, 3H), 1.03-1.17 (m, 6H), 1.38-1.44 (m, 2H), 2.08-2.11 (m, 2H), 5.47 (s, 2H, NH2), 5.85 (s, 2H, NH2), 7.17 (d, J=7.3Hz, 2H), 7.34 (dd, J=7.3,7.4Hz, 1H), 7.43 (dd, J=7.4, 7.5Hz, 2H); 13C (100 MHz, DMSO-d6) δ 14.72, 22.71, 28.95, 29.33, 31.67, 34.88, 107.88, 127.97, 129.71, 131.46, 136.82, 162.74, 162.85, 166.31; MS (ESITOF) m/z: Calcd. for C16H22N4: 270.38; found: 271.4. Anal. C, 71.08; H, 8.20; N, 20.72. Found: C, 71.11; H, 8.24; N, 20.77.
EXAMPLE 2
2,4-diamino-5-phenyl-6-(3-phenylpropyl)pyrimidine white crystals, mp 154-154.5° C. 1H (400 MHz, DMSO-d6) δ 1.74 (m, 2H), 2.13 (m, 2H), 2.13 (m, 2H), 2.41 (dd, J=7.6, 7.6Hz, 2H), 5.45 (s, 2H, NH2), 5.87 (s, 2H, NH2), 7.03 (d, J=7.3Hz, 2H), 7.11-7.23 (m, 5H), 7.33-7.36 (m, 1H), 7.40-7.44 (m, 2H); 13C (100 MHz, DSMO-d6) δ 30.65, 34.61, 35.80, 107.93, 126.42, 127.95, 128.99, 129.75, 131.43, 136.74, 142.64, 162.79, 162.87, 165.88; MS (ESITOF) m/z: Calcd. for C19H20N4: 304.40; found: 305.20. Anal. C, 74.97; H, 6.62; N, 18.41. Found: C, 74.85; H, 6.52; N, 18.46.
EXAMPLE 3
2,4-diamino-6-(3-methoxycarbonylpropyl)-5-phenylpyrimidine white crystals, mp 174-175° C. 1H (400 MHz, DMSO-d6) δ 1.77 (m, 2H), 2.10-2.18 (m, 4H), 3.49 (s, 3H), 6.06 (s, 2H, NH2), 6.15 (s, 2H, NH2), 7.16 (m, 2H), 7.33-7.37 (m, 1H), 7.42-7.46 (m, 2H); 13C (100 MHz, DMSO-d6) δ 24.18, 33.80, 33.93, 51.96, 108.05, 127.98, 129.76, 131.43, 136.67, 162.80, 162.90, 165.20, 173.80; MS (ESITOF) m/z: Calcd. for C15H18N4O2: 286.34; found: 287.18. Anal. C, 62.92; H, 6.34; N, 19.57. Found: C, 62.64; H, 6.39; N, 19.89.
EXAMPLE 4
2,4-diamino-5-(3-chlorophenyl)-6-(3-phenylpropyl)pyrimidine white crystals, mp 140-141° C. 1H (400 MHz, DMSO-d6) δ 1.75 (m, 2H), 2.10 (m, 2H), 2.43 (dd, J=7.4, 7.4Hz, 2H), 5.65 (s, 2H, NH2), 5.93 (s, 2H, NH2), 7.03 (d, J=7.3Hz, 2H), 7.10-7.14 (m, 2H), 7.19-7.22 (m, 3H), 7.38-7.44 (m, 2H), 13C (100 MHz, DSMO-d6) δ 30.50, 34.52, 35.71, 106.68, 126.44, 127.97, 128.98, 130.37, 131.26, 131.46, 134.14, 139.13, 142.54, 162.74, 162.96, 165.98; MS (ESITOF) m/z: Calcd. for C19H19CIN4: 338.84; found: 339.18. Anal. C, 67.35; H, 5.65; N, 16.53. Found: C, 67.34; H, 5.47; N, 16.50.
EXAMPLE 5
2,4-diamino-5-(3-chlorophenyl)-6-[3-(4-methoxyphenyl)propyl]pyrimidine white crystals, mp 111-111.5° C. 1H (400 MHz, DMSO-d6) δ 1.68 (m, 2H), 2.06 (dd, J=7.7, 7.7Hz, 2H), 2.34 (dd, J=7.4, 7.4Hz, 2H), 3.68 (s, 3H), 5.57 (s, 2H, NH2), 5.86 (s, 2H, NH2), 6.74 and 6.91 (AB quartet, J=8.5Hz, 4H), 7.08 (m, 1H), 7.16 (m,1H), 7.36-7.42 (m, 2H), 13C (100 MHz, DMSO-d6) δ 30.75, 34.44, 34.78, 55.77, 106.67, 114.39, 127.96, 129.87, 130.36, 131.24, 131.47, 134.14, 134.34, 139.09, 158.11, 162.74, 162.94, 166.13; MS (ESITOF) m/z: Calcd. for C20H21CIN4O: 368.87; found: 369.21. Anal. C, 65.12; H, 5.74; N, 15.19. Found: C, 65.22; H, 5.66; N, 15.24.
EXAMPLE 6
2,4-diamino-5-(3-chlorophenyl)-6-(3-methoxycarbonylpropyl)pyrimidine white crystals, mp 187.5-188° C. 1H (400 MHz, DMSO-d6) δ 1.71 (m, 2H), 2.09 (dd, J=7.5, 7.5Hz, 2H), 2.16 (dd, J=7.3, 7.3Hz, 2H), 3.48 (s, 3H), 5.60 (s, 2H, NH2), 5.90 (s, 2H, NH2), 7.10 (m, 1H), 7.18 (m, 1H), 7.37-7.45 (m, 2H); 13C (100 MHz, DMSO-d6) δ 24.05, 33.72, 33.88, 51.97, 106.82, 128.00, 130.40, 131.26, 131.50, 134.15, 139.07, 162.75, 162.98, 165.26, 173.86; MS (ESITOF) m/z: Calcd. for C15H17CIN4O2: 320.78, found: 321.13. Anal. C, 56.17; H, 5.34; N, 17.47. Found: C, 56.18; H, 5.35; N, 17.45.
EXAMPLE 7
2,4-diamino-5-(3-chlorophenyl)-6-[2-(3-phenoxypropyloxy)ethyl]pyrimidine white crystals, mp 93-94° C. 1H (400 MHz, DMSO-d6) δ 1.86 (m, 2H), 2.34 (m, 2H), 3.39 (dd, J=6.3, 6.3Hz, 2H), 3.56 (m, 2H), 3.93 (dd, J=6.3, 6.3Hz, 2H), 5.67 (s, 2H, NH2), 5.91 (s, 2H, NH2), 6.87-6.93 (m, 3H), 7.16 (d, J=7.0Hz, 1H), 7.25-7.29 (m, 3H), 7.37-7.45 (m, 2H), 13C (100 MHz, DMSO-d6) δ 29.90, 35.29, 65.21, 67.39, 69.77, 107.46, 115.25, 121.30, 128.02, 130.33, 130.42, 131.41, 131.48, 134.10, 138.93, 159.38, 162.77, 162.87, 163.35; MS (ESITOF) m/z: Calcd. for C21H23CIN4O2: 398.89; found: 399.40. Anal. C, 63.23; H, 5.81; N, 14.05. Found: C, 63.15; H, 5.81; N, 14.04.
2. Enzyme Inhibitory, Antimalarial and Other Properties of the Invented Compounds
2.1 Determination of Enzyme Inhibition Constants (Ki)
It is an object of this invention to provide 2,4-diaminopyrimidine derivative compounds, and pharmaceutically acceptable salts thereof, for substantially inhibiting dihydrofolate reductase enzymes. Enzymes, comprising dihydrofolate reductase of Plasmodium falciparum, wild type, single (S108N), double (C59R+S108N), triple (N51+C59R+S108N, C59R+S108N+1164L), and quadruple (N51+C59R+S108N+I164L) mutants, were prepared from E. coli expression system (E. coli BL21 (DE3)pLysS) containing the corresponding genes. The activity of the enzymes was determined spectrophotometrically at 25° C. The reaction (1 mL) contained 1×DHFR buffer (50 mM TES, pH 7.0, 75 mM β-mercaptoethanol, 1 mg/mL Bovine Serum Albumin), 100 μM each of the substrate dihydrofolate and cofactor NADPH, and appropriate amount of affinity-purified enzyme to initiate the reaction (0.001-0.005 units in phosphate buffer containing 50 mM KCl).
The inhibition of the enzymes with the invented compounds was investigated in a 96 well plate with 200 μL of the above mixture in the presence of antifolate. The kinetics was followed at 340 nm. The Ki values of the inhibitors for the wild type and mutant enzymes were determined by fitting to the equation IC50=Ki (1+([S]/Km)), where IC50 is the concentration of inhibitor which inhibits 50% of the enzyme activity under the standard assay condition and Km is the Michaelis constant for the substrate dihydrofolate.
The inhibition constants (Ki) of the invented compounds against wild type and mutants PfDHFR are as summarized in Table 1.
TABLE 1
Inhibition constants (Ki) of 2,4-diaminopyrimidine derivative
compounds for binding with wild type and mutant PfDHFRs
Ki (nM)
N51I + C59R + N51I + C59R +
Example Wild type S108N C59R + S108N C59R + S108N S108N + I164L S108N + I164L
Pyr 0.6 ± 0.2 28.6 ± 2.3  53.9 ± 6.5  67.1 ± 4.2  112 ± 17  385 ± 163
1 0.3 ± 0.1 1.2 ± 0.3 0.7 ± 0.3  0.4 ± 0.02 0.7 ± 0.2 1.4 ± 0.5
2 0.5 ± 0.0 0.9 ± 0.2 2.4 ± 0.1 1.1 ± 0.1 1.9 ± 0.1 4.7 ± 0.9
3 0.6 ± 0.0 1.8 ± 0.2 5.5 ± 0.5 3.3 ± 0.6 15 ± 3  24 ± 2 
4 1.2 ± 0.2 3.0 ± 0.6 4.2 ± 0.2 2.0 ± 0.2 2.2 ± 0.3 2.0 ± 0.8
5 2.2 ± 0.6 4.0 ± 0.2 6.0 ± 0.6 1.3 ± 0.1 2.9 ± 0.3 2.0 ± 0.4
6 0.5 ± 0.0 1.7 ± 0.1 2.8 ± 0.2 0.8 ± 0.2 1.8 ± 0.4 2.7 ± 1.2
7 0.4 ± 0.2 1.8 ± 0.3 1.9 ± 0.4 0.7 ± 0.1 1.3 ± 0.4 1.7 ± 0.2

2.2 Determination of Antimalarial Activities (IC50)
It is an object of this invention to provide 2,4-diaminopyrimidine derivative compounds, and pharmaceutically acceptable salts thereof, having antimalarial activity, including activity against drug-resistant malaria both by themselves and in synergistic combinations with sulfonamides and/or other agents. P. falciparum strains were used in this study. P. falciparum strains were maintained continuously in human erythrocytes at 37° C. under 3% CO2 in RPMI 1640 culture media supplemented with 25 mM HEPES, pH 7.4, 0.2% NaHCO3, 40 μg/mL gentamicin and 10% human serum.
In vitro antimalarial activity was determined by using [3H]-hypoxanthine incorporation method. The drugs were initially dissolved in DMSO and diluted with the culture media. Aliquots (25 μL) of the drug of different concentrations were dispensed in 96-well plates and 200 μL of 1.5% cell suspension of parasitized erythrocytes containing 1-2% parasitemia were added. The final concentration of DMSO (0.1%) did not affect the parasite growth. The mixtures were incubated in a 3% CO2 incubator at 37° C. After 24 h of incubation, 25 μL (0.25 μCi) of [3H]-hypoxanthine were added to each well. The parasite cultures were further incubated under the same condition for 18-24 h. DNA of parasites was harvested onto glass filter paper. The filters were air-dried and 20 μL liquid scintillation fluid was added. The radioactivity on the filters was then measured using a microplate scintillation counter. The concentration of inhibitor which inhibited 50% of the parasite growth (IC50) was determined from the sigmoidal curve obtained by plotting the percentages of [3H]-hypoxanthine incorporation against drug concentrations. Examples of the invented compounds in this series with active antimalarial activity against wild type and in particular against parasites carrying single, double, triple, and quadruple mutant enzymes are as summarized in Table 2.
TABLE 2
Anti-plasmodial activities (IC50) of 2,4-
diaminopyrimidine derivative compounds against
Plasmodium falciparum with wild type (TM4/8.2) and
the mutant enzymes: K1CB1 (C59R + S108N), W2
(N51I + C59R + S108N), Csl-2 (C59R + S108N +
I164L), and V1/S (N51I + C59R + S108N + I164L)
Ex-
am- IC50 (μM)
ple  TM4/8.2 K1CB1 W2 Csl-2 V1/S
Pyr 0.08 ± 0.01 30.9 ± 8.4  73.1 ± 7.4 41.7 ± 14.8 >100
1 0.06 ± 0.02 1.3 ± 0.1  2.3 ± 0.7 3.0 ± 1.1 6.4 ± 2.9
2 0.21 ± 0.06 2.3 ± 0.6  2.7 ± 0.6 2.7 ± 0.7 8.6 ± 2.4
3 0.39 ± 0.06 31.3 ± 5.5  >100 34 ± 11 >100
4 0.67 ± 0.06 3.0 ± 0.8  4.3 ± 0.7 3.6 ± 0.4 5.7 ± 2.5
5 0.41 ± 0.05 2.7 ± 0.6  4.0 ± 0.3 2.7 ± 0.3 4.7 ± 0.6
6 0.79 ± 0.10 36.3 ± 6.1   >50 4.9 ± 1.2  >50
7 0.35 ± 0.08 3.3 ± 0.1  4.5 ± 0.4 2.9 ± 0.4 7.1 ± 4.2

2.3 Determination of Cytotoxicity to Mammalian Cells (IC50)
Cytotoxicity tests of the invented compounds against African green monkey kidney fibroblast (Vero cells), Human epidermoid carcinoma (KB) cells, Human breast cancer (BC) cells were performed according to the protocol described by Skehan et al (1990).
These compounds have selectivity against malaria parasites with no or less effect on mammalian cell lines. The cytotoxicity to three mammalian cell lines (Vero, KB, and BC cells) is as summarized in Table 3.
TABLE 3
Cytotoxicity of the 2,4-diaminopyrimidine derivative
compounds to mammalian cells (IC50)
IC50 (μM)
Example Vero Cells KB cells BC Cells
Pyr 32 109 40.0
1 55 113 268.0
2 >50 150 250.0
3 20 71 500.0
4 2.1 1.6 1.6
5 3 15 3.0
6 20 9.3 22.8
7 15 6.4 4.9

2.4 Determination of Antibacterial Activities (IC50)
Antibacterial activity of the invented compounds was determined by incubation of suspension of bacteria, Staphylococcus aureus and E. coli with a serial dilution of the drugs for 20 hours in a 96-well plate. Bacterial growth inhibition was determined by spectrophotometer at 600 nm. The IC50-values was determined from the sigmoidal curve obtained by plotting the percentages of bacterial growth against drug concentrations.
These compounds have selectivity against malaria parasites with no or less effect on bacteria. The antibacterial activities to S. aureus, and E. coli are as summerized in Table 4.
TABLE 4
Antibacterial activities (IC50) of 2,4-diaminopyrimidine
derivative compounds
IC50 (μM)
Example S. aureus E. coli
Trimethoprim 6.0 2.3
1 >10 >10
2 >50 >50
3 >50 >50
4 >50 >50
5 38.0 >50
6 >50 >50
7 >50 >50
REFERENCES
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  • 11. Russell, P. B., Hitchings, G. H. 2,4-Diaminopyrimidines as Antimalarials. III. 5-Aryl Derivatives. J. Am. Chem. Soc. 73: 3763-3770 (1951)
  • 12. Chase, B. H., Walker, J. The Preparation of Enol Ethers from Certain β-Keto-nitriles. J. Chem. Soc. 3518-3525 (1953)
  • 13. Blaney, J. M., Hansch, C., Silipo, C., Vittoria, A. Structure-Activity Relationships of Dihydrofolate Reductase Inhibitors. Chem. Rev. 84: 333-407 (1984)
  • 14. McKie, J. H., Douglas, K. T., Chan, C., Roser, S. A., Yates, R., Read, M., Hyde, J. E., Dascombe, M. J., Yuthavong, Y., Sirawaraporn, W. Rational Drug Design Approach for Overcoming Drug Resistance: Application to Pyrimethamine resistance in Marlaria. J. Med. Chem. 41: 1367-1370 (1998)
  • 15. Barlin, G. B., Kotecka, B., Rieckmann, K. H. Potential Antimalarials. XXII. Some 2,4-Diamino-5-(3- and 4-trifluoromethylphenyl and 3,4-methylenedioxyphenyl) pyrimidines. Aust. J. Chem. 49: 647-650 (1996)
  • 16. Tarnchompoo, B., Sirichaiwat, C., Phupong, W., Intaraudom, C., Sirawaraporn, W., Kamchonwongpaisan, S., Vanichtanankul, J., Thebtaranonth, Y., Yuthavong, Y. Development of 2,4-Diaminopyrimidines as Antimalarials Based on Inhibition of the S108N and C59R+S108N Mutants of Dihydrofolate Reductase from Pyrimethamine-Resistant Plasmodium falciparum. J. Med. Chem. 45: 1244-1252 (2002)
  • 17. Trager, W., Jensen, J. B. Human Malaria Parasites in Continuous Culture. Science: 193: 673-675 (1976)
  • 18. Desjardins, R. E., Canfield, C. J., Haynes, J. D., Chulay, J. D. Quantitative Assessment of Antimalarial Activity in vitro by a Semiautomated Microdilution Techniques. Antimicrob. Agents Chemother. 16: 710-718 (1979)
  • 19. Skehan, P., Storeng, R., Scudiero, D., Monks, A., McMahon, J.; Vistica, D., Warren, J. T., Bokesch, H., Kenney, S., Boyd, M. R. New Colorimetric Cytotoxicity Assay for Anticancer-Drug Screening. J. Natl. Cancer Inst. 82: 1107-1112 (1990)

Claims (14)

1. A method for inhibiting a mutant dihydrofolate reductase (DHFR) protein in drug-resistant malaria, comprising administering a pharmaceutical composition which comprises a compound of formula:
Figure US07371758-20080513-C00002
wherein R1 is a hydrogen or halogen atom, and R2 is selected from the group consisting of: C5 to C6 alkyl; C1 to C3 alkyl having a terminal aromatic substituent or an alkoxycarbonyl substituent; and an aryloxyalkoxyalkyl group, wherein said malaria is caused by Plasmodium falciparum comprising the mutant DHFR protein with at least three mutations, wherein the mutations are selected from the group consisting of N51I, C59R, S108N, and I164L.
2. The method of claim 1, wherein the Plasmodium falciparum is resistant to antifolate compounds.
3. The method of claim 2, wherein the Plasmodium falciparum is resistant to pyrimethamine.
4. The method of claim 1, wherein said Plasmodium falciparum DHFR protein comprises at least four mutations.
5. The method of claim 1, wherein said at least three mutations comprise C59R, S108N, and I164L.
6. The method of claim 1, wherein said at least three mutations comprise N51I, C59R, and S108N.
7. The method of claim 4, wherein said at least four mutations comprise N51I, C59R, S108N, and I164L.
8. The method of claim 1, wherein R2 is 3-phenylpropyl, 3-(4-methoxyphenyl)propyl, 3-methoxycarbonylpropyl or 2-(3-phenoxypropyloxy)ethyl.
9. The method of claim 1, wherein R1 is chloro.
10. The method of claim 1, wherein the compound is 2,4-diamino-5-(3-chlorophenyl)-6-(3-phenylpropyl)pyrimidine, 2,4-diamino- 5-(3-chlorophenyl)-6-[3-(4-methoxyphenyl)propyl]pyrimidine, 2,4-diamino-5-(3-chlorophenyl)-6-(3-methoxycarbonylpropyl)pyrimidine, or 2,4-diamino-5-(3-chlorophenyl)-6-[2-(3-phenoxypropyloxy)ethyl]pyrimidine.
11. The method of claim 1, wherein R2 is n-hexyl, 3-phenylpropyl, or 3-methoxycarbonylpropyl.
12. The method of claim 1, wherein R1 is hydrogen.
13. The method of claim 12, wherein the compound is 2,4-diamino-5-phenyl-6-(n-hexyl)pyrimidine, 2,4-diamino-5-phenyl-6-(3-phenylpropyl)pyrimidine, or 2,4-diamino-5-phenyl-6-(3-methoxycarbonylpropyl)pyrimidine.
14. A method for inhibiting a mutant dihydrofolate reductase (DHFR) protein in drug-resistant malaria, comprising administering a pharmaceutical composition which comprises a compound of formula:
Figure US07371758-20080513-C00003
wherein R1 is a hydrogen or halogen atom, and R2 is selected from the group consisting of: C5 to C6 alkyl; C1 to C3 alkyl having a terminal aromatic substituent or an alkoxycarbonyl substituent; and an aryloxyalkoxyalkyl group, wherein said malaria is caused by Plasmodium falciparum comprising the mutant DHFR protein with at least four mutations selected from the group consisting of N51I, C59R, S108N, and I164L.
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